I love the conversation and debate that goes on here but I don’t always go back to check if people responded to my comments. Wouldn’t comment notifications be a really helpful feature of HN?
Yes, but HN is a zero-distraction distraction: It's a workplace procrastination tool that doesn't let the user veer too far from their work. You can see this in the anti-procrast settings and the lack of any advertising here (both of which are very nice features I use regularly). If HN had notifications it'd lead on a slippery slope to HN being a social network instead of a news aggregator, and I don't think anybody wants that.
That's a third-party site though. If HN did a very simple thing: publish some data in RSS feed format, then an RSS reader (e.g. one living in your browser as an extension) would provide a notification interface.